I'm using Rosetta 3.4 and I want to make a homology model of a GPCR protein -> I know very well how the model should look like.
This is the input I'm using:
-database /opt/soft/rosetta3.4/rosetta_database \
-in:file:fasta mc4.fasta \
-in:file:native s1p.pdb \
-in:file:template_pdb s1p.pdb \
-in:file:psipred_ss2 mc4.psipred_ss2 \
-frag3 mc4_03 \
-frag9 mc4_09 \
-loops:frag_files mc4_09 mc4_03 none \
-loops:frag_sizes 9 3 1 \
-loops:remodel quick_ccd \
-loops:refine refine_ccd \
-in:file:alignment alignment.aln \
-cm:aln_format general \
-out:nstruct 1 \
-out:file:silent mc4.silent.out \
The template pdb is s1p.txt and the model is mc4_S_001.txt.
What has gone wrong? Any ideas?